Top 5 Free Research Programs

Throughout graduate studies and into a research career, software, internet sites, and digital tools are required for effective communication of scientific discovery. Here are five of my favourite, some of their competitors and examples of their application.

  1. R 

Everyone has their favourite statistics package; I use R. Statistica is another I have tried with a good user interface. However, once learning some basics in R it can be a great tool for more complex applications. Many others utilize the package, its free, and the help articles are well written with examples. Beyond choosing the right statistical package for you, success can be developed in becoming friends with those who understand the wacky world of analyzing numbers!

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An example of a tutorial demonstrating some very basic R code

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A screenshot of my favourite R help site (http://www.statmethods.net/advstats/factor.html)

  1. Mendeley 

Projects can feel daunting to start out with especially when the first thing you do is search your favourite database to find hundreds or thousands of hits. No worries; Mendeley will assist in your citation needs! This citation manager collects information about a paper either from an online source or a PDF copy you have saved on to your desktop manager. Then you can import the citations into your paper as you write, along with the bibliography. There are certainly other options (such as Zotero and EndNote). However, Mendeley has a larger storage space that is capable of holding PDF files.

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Exert of Mendeley Desktop

  1. Avagadro and Jmol 

You do not need to know Avagadro’s number to be able to run this program! Avagadro (the program) is a free online software used to input chemical structures and Jmol then functions to create beautiful 3D images of molecules. These programs work together where the user interface is in Avagadro but Jmol is needed as a support program. There are numerous ways of using these tools but one favourite, is to create electronegative 3D maps of molecules (See Figure). This can support proposed mechanisms of action or bring about ideas of regions that may be reactive. Lastly, these points can all be presented nicely on a PowerPoint slide, decorated by the visual of the substance.

EC 3

An example of an electronegativity map of ethyl carbamate, a known rodent carcinogen. The blue low electronegativity highlights a reactive ethyl functional group, believed to be capable of binding to DNA (Jmol).

  1. Audacity 

Free and great potential for fun! Audacity is a recording program capable of integrating tracks, removing bloopers, and adding effects. Beyond these basic tools, Audacity has an applicable place in the scientific community. Podcasts are a common communication tool to share information with others in the field or bored commuters battling the Toronto traffic. For more personal use, Audacity can be used to quickly record presentations. Listening to yourself as you travel or walk around the neighborhood can be an effective tool to practice a conference presentation. One reason listening to a recording could be beneficial is to retain not just the content but also the calm intonation. If you are uncomfortable with hearing your own voice, finding a friend to record for you, or even recommending this tool to a nervous group member could smooth the preparation for a presentation!

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Audacity in full swing: collected pitches measured along an x-axis representing time.

 

  1. ChemSpider (online)

This is a website which can be lovely when dealing with long chemical names. Input your compounds IUPAC name and the program is capable of providing you a structural representation. It is recommended that one checks the structures to ensure they are correct. However, it is often much easier to identify a mistake than begin drawing a symmetrical structure with as great a digital ease as ChemSpider.

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Copper(2+) phthalocyanine-29,31-diide (phthalocyanine blue): a chemical that is structurally interesting and compound that is beautifully coloured.

As you explore and try new programs, enjoy the ease and efficiency of completing tasks. As you think of programs you have used before, create new ways to use these tools. As you learn of knowledge gaps, consider creating new tools to benefit research in the scientific community.

Feature image from: http://avocaventures.com/predictive-html-css-php-code-compiler/

Adelle is a master’s candidate in toxicology and has received her B.Sc. in Integrated Science with Biochemistry. Through her studies, she gained a reputation as an ideas person, an encourager to her peers, and a hard worker. She aims to continue exploring, innovating, and inventing at every opportunity that arises.

 

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